Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 24 of 173
Found at i:6413803 original size:25 final size:24
Alignment explanation
Indices: 6413702--6413822 Score: 77
Period size: 25 Copynumber: 4.8 Consensus size: 24
6413692 TCTTCAAGTA
* *
6413702 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
* *
6413727 TTTTTAATTACCAAGTTTTTTTATCAAA-
1 TTTTTCA-T--CAAG-TCTTTTAT-AAAG
*
6413755 TTTTTGCAGCAAGTTCTTTT-TAAAG
1 TTTTT-CATCAAG-TCTTTTATAAAG
*
6413780 TTTTTCATCAAGTCTTTTCATAAAA
1 TTTTTCATCAAGTCTTTT-ATAAAG
*
6413805 TTTTCCATCAAGT-TTTTA
1 TTTTTCATCAAGTCTTTTA
6413823 ATCATTTCGT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
23 7 0.09
24 13 0.17
25 28 0.36
26 11 0.14
28 16 0.21
29 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTTTCATCAAGTCTTTTATAAAG
Found at i:6414217 original size:16 final size:16
Alignment explanation
Indices: 6414196--6414231 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
6414186 TTTGGTTCGC
6414196 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6414212 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6414228 TGTA
1 TGTA
6414232 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6414488 original size:18 final size:17
Alignment explanation
Indices: 6414467--6414501 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6414457 TTATTATTAA
*
6414467 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6414485 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6414502 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6414555 original size:157 final size:157
Alignment explanation
Indices: 6414354--6414638 Score: 507
Period size: 157 Copynumber: 1.8 Consensus size: 157
6414344 TAGAATACCC
* *
6414354 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
6414419 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
6414484 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
6414511 TTAGCAAAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
6414576 ATATCAATAATAAATAATTTAATCATATTTAAATATAATTATTATTAAATATATTATAATTAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA
6414639 TAAGGAACCA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 121 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAAAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:6414637 original size:15 final size:16
Alignment explanation
Indices: 6414604--6414638 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6414594 TTAATCATAT
*
6414604 TTAAATATAATTATTA
1 TTAAATATAATTATAA
6414620 TTAAATAT-ATTATAA
1 TTAAATATAATTATAA
6414635 TTAA
1 TTAA
6414639 TAAGGAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATATAATTATAA
Found at i:6430320 original size:3 final size:3
Alignment explanation
Indices: 6430314--6430373 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
6430304 TTTTTTAGTA
6430314 ATT ATT ATT ATT ATT ATT ATT -TCT ATT ATT ATT ATT -TT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
*
6430357 ATTT ATC A-T ATT ATT AT
1 A-TT ATT ATT ATT ATT AT
6430374 ACGATAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 6 0.12
3 39 0.80
4 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6432575 original size:56 final size:57
Alignment explanation
Indices: 6432515--6432637 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 57
6432505 CAATTTTGGT
* *
6432515 CTGTCAATGGCTGG-AACCAGAATACGAAAAAAA-GAAAAAAAA-ATTTGGGTGCTGGC
1 CTGTCAATGGCCGGCAACCAG--TACGAAAAAAAGGAAAAAAAATATTTGGGTGCTGAC
* *
6432571 CTGTCAATGGCCGGCACCCAGTACGAAAAAAAGGAAAAAAAATTTTTGGGTGCTGAC
1 CTGTCAATGGCCGGCAACCAGTACGAAAAAAAGGAAAAAAAATATTTGGGTGCTGAC
*
6432628 CTATCAATGG
1 CTGTCAATGG
6432638 GGTGCACCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
55 11 0.19
56 22 0.37
57 26 0.44
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (57 bp):
CTGTCAATGGCCGGCAACCAGTACGAAAAAAAGGAAAAAAAATATTTGGGTGCTGAC
Found at i:6432635 original size:57 final size:55
Alignment explanation
Indices: 6432537--6432661 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 55
6432527 GGAACCAGAA
* *
6432537 TACGAAAAAAAGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCG-GCACCCAG
1 TACGAAAAAAAGAAAAAAAAATTTGGGTGCTGACCTATCAATGG-CGTGCACCCAG
* *
6432592 TACGAAAAAAAGGAAAAAAAATTTTTGGGTGCTGACCTATCAATGGGGTGCACCCAG
1 TACGAAAAAAA-GAAAAAAAA-ATTTGGGTGCTGACCTATCAATGGCGTGCACCCAG
6432649 TACAGTAAAAAAA
1 TAC-G-AAAAAAA
6432662 ATTCGAGTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
55 11 0.18
56 10 0.16
57 32 0.52
58 1 0.02
59 7 0.11
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (55 bp):
TACGAAAAAAAGAAAAAAAAATTTGGGTGCTGACCTATCAATGGCGTGCACCCAG
Found at i:6433145 original size:20 final size:20
Alignment explanation
Indices: 6433122--6433159 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6433112 AAAATGTAAA
6433122 AATAAAAGAAATATTTACAT
1 AATAAAAGAAATATTTACAT
6433142 AATAAAAGAAATATTTAC
1 AATAAAAGAAATATTTAC
6433160 GCTGGGGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (20 bp):
AATAAAAGAAATATTTACAT
Found at i:6435529 original size:43 final size:43
Alignment explanation
Indices: 6435472--6435627 Score: 181
Period size: 43 Copynumber: 3.6 Consensus size: 43
6435462 ATTGATTTGA
6435472 GATTTACGTGTAAGAACATGTCTGGGACATTGGCATCGTATAT
1 GATTTACGTGTAAGAACATGTCTGGGACATTGGCATCGTATAT
* *
6435515 GATTTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATAT
1 GATTTACGTGTAAGAACATGTCTGGGACATTGGCATCGTATAT
* * * * * * *
6435558 GATTTACGTATAAGACCTTGTCTGGAACAGTGGCATAGATATTT
1 GATTTACGTGTAAGAACATGTCTGGGACATTGGCATCG-TATAT
* *
6435602 GA-TTACATGCAAG-ACATCGTCTGGGA
1 GATTTACGTGTAAGAACAT-GTCTGGGA
6435628 TGTAGGCATT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 2 0.02
43 88 0.92
44 6 0.06
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTTACGTGTAAGAACATGTCTGGGACATTGGCATCGTATAT
Found at i:6437012 original size:31 final size:34
Alignment explanation
Indices: 6436987--6437053 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
6436977 TTTCAAAGTT
6436987 CTTT-TATTT-CTATTCCATTTATTTCAAAACTCA
1 CTTTCTATTTCCTATTCCATTTATTTC-AAACTCA
* *
6437020 CTTTCTTTTTCCTATTCCATTTATTTCAATCTCA
1 CTTTCTATTTCCTATTCCATTTATTTCAAACTCA
6437054 TTTATTGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 4 0.13
34 10 0.33
35 16 0.53
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (34 bp):
CTTTCTATTTCCTATTCCATTTATTTCAAACTCA
Found at i:6437152 original size:52 final size:52
Alignment explanation
Indices: 6437082--6437558 Score: 670
Period size: 52 Copynumber: 9.2 Consensus size: 52
6437072 CTTACACTTT
* * * *
6437082 TTTTTTTCATTCAGTCTCATTTGTTTTAAATTTTTTTCCTACATCTAACA-CT
1 TTTTTTTCATTCAATCTCATTTATTTTAAA-TTCTTTCCTACATCTAACACCC
* * *
6437134 TTTTTTTCATTCAATCTCATTTATTTCAAAATTTTTTCCTACATCTAACAACCTT
1 TTTTTTTCATTCAATCTCATTTATTT-TAAATTCTTTCCTACATCTAAC-ACC-C
*
6437189 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACTC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
6437241 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
6437293 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
*
6437345 TTTTTTTCATTCAATCTC---------AAATTCTTTCCAACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
6437388 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
* *
6437440 -TTTTTTCATTCAATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAA-TTCTTTCCTACATCTAACACCC
* * *
6437492 TTTTTTTTCATTCAATCTCATTTATTTTAGATTTTTTTTTTCTACATCTAACACCC
1 -TTTTTTTCATTCAATCTCATTTATTTTA-A--ATTCTTTCCTACATCTAACACCC
6437548 TTTTTTTCATT
1 TTTTTTTCATT
6437559 TTCGTTTCTA
Statistics
Matches: 391, Mismatches: 15, Indels: 35
0.89 0.03 0.08
Matches are distributed among these distances:
43 42 0.11
51 28 0.07
52 208 0.53
53 6 0.02
54 47 0.12
55 39 0.10
56 21 0.05
ACGTcount: A:0.24, C:0.23, G:0.01, T:0.52
Consensus pattern (52 bp):
TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC
Found at i:6437361 original size:24 final size:24
Alignment explanation
Indices: 6437334--6437404 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
6437324 TCTTTCCTAC
6437334 ATCTAACACCCTTTTTTTCATTCA
1 ATCTAACACCCTTTTTTTCATTCA
* * *
6437358 ATCTCAA-A---TTCTTTCCA-AC-
1 ATCT-AACACCCTTTTTTTCATTCA
6437377 ATCTAACACCCTTTTTTTCATTCA
1 ATCTAACACCCTTTTTTTCATTCA
6437401 ATCT
1 ATCT
6437405 CATTTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 1 0.03
21 7 0.21
22 7 0.21
23 1 0.03
24 9 0.26
25 2 0.06
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.44
Consensus pattern (24 bp):
ATCTAACACCCTTTTTTTCATTCA
Found at i:6437392 original size:147 final size:147
Alignment explanation
Indices: 6437082--6437511 Score: 621
Period size: 147 Copynumber: 2.8 Consensus size: 147
6437072 CTTACACTTT
* * * *
6437082 TTTTTTTCATTCAGTCTCATTTGTTTTAAATTTTTTTCCTACATCTAACA-CTTTTTTTTCATTC
1 TTTTTTTCATTCAATCTCATTTATTTTAAA-TTCTTTCCTACATCTAACACCCTTTTTTTCATTC
*
6437146 AATCTCATTTATTTCAAAATTTTTTCCTACATCTAACAACCTTTTTTTTTCATTCAATCTCATTT
65 AATCTCATTTATTT-AAAATTTTTTCCTACATCTAAC-ACC-CTTTTTTTCATTCAATCTC----
* *
6437211 ATTTTAAATTCTTTCCTACATCTAACACTC
123 -----AAATTCTTTCCAACATCTAACACCC
6437241 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCCTTTTTTTCATTCA
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCCTTTTTTTCATTCA
* *
6437306 ATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCCTTTTTTTCATTCAATCTCAAATTCTT
66 ATCTCATTTATTTAAAATTTTTTCCTACATCTAACACCCTTTTTTTCATTCAATCTCAAATTCTT
6437371 TCCAACATCTAACACCC
131 TCCAACATCTAACACCC
6437388 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCC-TTTTTTCATTCA
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCCTTTTTTTCATTCA
*
6437452 ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACCCTTTTTTTTCATTCAATCTCA
66 ATCTCATTTATTT-AAAATTTTTTCCTACATCTAACACCC-TTTTTTTCATTCAATCTCA
6437512 TTTATTTTAG
Statistics
Matches: 256, Mismatches: 12, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
146 25 0.10
147 98 0.38
148 19 0.07
156 18 0.07
157 3 0.01
158 38 0.15
159 55 0.21
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (147 bp):
TTTTTTTCATTCAATCTCATTTATTTTAAATTCTTTCCTACATCTAACACCCTTTTTTTCATTCA
ATCTCATTTATTTAAAATTTTTTCCTACATCTAACACCCTTTTTTTCATTCAATCTCAAATTCTT
TCCAACATCTAACACCC
Found at i:6437574 original size:55 final size:56
Alignment explanation
Indices: 6437421--6437558 Score: 178
Period size: 54 Copynumber: 2.6 Consensus size: 56
6437411 TTTTAAATTC
** * *
6437421 TTTCCTACATCTAACACCC--TTTTTTCATTCAATCTCATTTATTTCA-A-ATTTT
1 TTTCCTACATCTAACACCCTTTTTTTTCATTCAATCTCATAGATTTTAGATTTTTT
**
6437473 TTTCCTACATCTAACACCCTTTTTTTTCATTCAATCTCATTTATTTTAGATTTTTT
1 TTTCCTACATCTAACACCCTTTTTTTTCATTCAATCTCATAGATTTTAGATTTTTT
*
6437529 TTTTCTACATCTAACACCC-TTTTTTTCATT
1 TTTCCTACATCTAACACCCTTTTTTTTCATT
6437559 TTCGTTTCTA
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
52 19 0.24
54 26 0.33
55 12 0.15
56 22 0.28
ACGTcount: A:0.22, C:0.24, G:0.01, T:0.53
Consensus pattern (56 bp):
TTTCCTACATCTAACACCCTTTTTTTTCATTCAATCTCATAGATTTTAGATTTTTT
Found at i:6440748 original size:113 final size:114
Alignment explanation
Indices: 6440589--6440808 Score: 354
Period size: 114 Copynumber: 1.9 Consensus size: 114
6440579 ACCTGAAAAA
* * *
6440589 TTTTTCCCCCAAAAAGGTGGTGTCGGCCATTGGCAGGCCACCACC-AAATTTTTTTTTACTTTTT
1 TTTTTCCCCAAAAAAGGTGGTGCCGGCCATTGGCAGACCACCACCAAAATTTTTTTTTACTTTTT
* *
6440653 TCGTATACTGATACCTGCTATTGACACG-AAAAAAGTAAAAAAAAATAT
66 TCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAATAT
*
6440701 TTTTTCCACCAAAAAAGGTGGTGCCGGCCATTGGCAGACCATCACCAAAATTTTTTTTTACTTTT
1 TTTTTCC-CCAAAAAAGGTGGTGCCGGCCATTGGCAGACCACCACCAAAATTTTTTTTTACTTTT
*
6440766 TTCGTATACTGATACTTGATACTGACACGAAAAAAAGTAAAAA
65 TTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAA
6440809 TTTTTTTATT
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
112 7 0.07
113 34 0.35
114 44 0.45
115 13 0.13
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (114 bp):
TTTTTCCCCAAAAAAGGTGGTGCCGGCCATTGGCAGACCACCACCAAAATTTTTTTTTACTTTTT
TCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAATAT
Found at i:6440969 original size:54 final size:57
Alignment explanation
Indices: 6440857--6441006 Score: 153
Period size: 61 Copynumber: 2.6 Consensus size: 57
6440847 AAACTCGAAT
*
6440857 TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAAAATTGTTTTTTTCC
1 TTTTTTT-C-GTACTGGGTGCCGGCCATTGACAGGCCAGCATCC--AAAAA-T-TTTTTTTCA
* * *
6440920 TTTTTTTCGTACTGGGTGTCGGTCATTGACAGGCCAGCA-CC-CAAATTTTTTTT-A
1 TTTTTTTCGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTTTTTCA
** *
6440974 TTTTTTTCGTACTTTTGTGCCGACCATTGACAG
1 TTTTTTTCGTAC-TGGGTGCCGGCCATTGACAG
6441007 ACGAAAACTC
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
54 12 0.16
55 22 0.29
56 1 0.01
57 3 0.04
60 2 0.03
61 29 0.38
62 1 0.01
63 7 0.09
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (57 bp):
TTTTTTTCGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAAATTTTTTTTCA
Found at i:6442589 original size:21 final size:24
Alignment explanation
Indices: 6442540--6442592 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
6442530 TTAATGTTCA
6442540 TTTTAATCACCCAACTTTTATAACT
1 TTTTAATCACCCAACTTTTAT-ACT
*
6442565 TTTTAATCACTC-A-TTTTAT-CT
1 TTTTAATCACCCAACTTTTATACT
6442586 TTTTAAT
1 TTTTAAT
6442593 TTCCTTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 9 0.33
23 6 0.22
24 1 0.04
25 11 0.41
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAATCACCCAACTTTTATACT
Found at i:6447516 original size:6 final size:6
Alignment explanation
Indices: 6447507--6447564 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
6447497 TAAGGCTTTC
*
6447507 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTCTCTA --TTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
6447553 TTTTTA TTTTTA
1 TTTTTA TTTTTA
6447565 AAAAATATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 3 0.07
5 2 0.04
6 41 0.89
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:6448231 original size:12 final size:12
Alignment explanation
Indices: 6448216--6448246 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6448206 TAATTAATGT
6448216 TATTATTATTAC
1 TATTATTATTAC
*
6448228 TATTATTATTGC
1 TATTATTATTAC
6448240 TATTATT
1 TATTATT
6448247 TATATATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:6448385 original size:20 final size:22
Alignment explanation
Indices: 6448362--6448408 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
6448352 ATTAATTCAC
6448362 TATTTTTTTA-TTAATATTA-T
1 TATTTTTTTACTTAATATTATT
* *
6448382 TA-TTATTTACTTATTATTATT
1 TATTTTTTTACTTAATATTATT
6448403 TATTTT
1 TATTTT
6448409 AATTTCAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 3 0.14
22 2 0.10
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTTACTTAATATTATT
Found at i:6448395 original size:14 final size:14
Alignment explanation
Indices: 6448378--6448404 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6448368 TTTATTAATA
6448378 TTATTATTATTTAC
1 TTATTATTATTTAC
6448392 TTATTATTATTTA
1 TTATTATTATTTA
6448405 TTTTAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTAC
Found at i:6450943 original size:16 final size:16
Alignment explanation
Indices: 6450924--6450955 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6450914 GTAGTGGACT
6450924 TTTGTGGACTTTTCAA
1 TTTGTGGACTTTTCAA
6450940 TTTGTGGACTTTTCAA
1 TTTGTGGACTTTTCAA
6450956 CCATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTGTGGACTTTTCAA
Found at i:6451355 original size:12 final size:12
Alignment explanation
Indices: 6451338--6451364 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6451328 AATAAATCAT
6451338 ATATGTATATTA
1 ATATGTATATTA
6451350 ATATGTATATTA
1 ATATGTATATTA
6451362 ATA
1 ATA
6451365 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:6451728 original size:25 final size:25
Alignment explanation
Indices: 6451693--6451740 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6451683 TCTAATCTCA
*
6451693 CCGCTATAGT-ATTCAATCTCACCAG
1 CCGCTACAGTAATT-AATCTCACCAG
6451718 CCGCTACAGTAATTAATCTCACC
1 CCGCTACAGTAATTAATCTCACC
6451741 GCCACCACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.27
Consensus pattern (25 bp):
CCGCTACAGTAATTAATCTCACCAG
Found at i:6455705 original size:26 final size:26
Alignment explanation
Indices: 6455651--6455705 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
6455641 TTTATACTCC
**
6455651 TTTCATTTTATTAAACCTCTATTTTA
1 TTTCATTTTATTAAACCTCTATTCCA
*
6455677 TTTCATTTTATTACAA-GTCTATTCCA
1 TTTCATTTTATTA-AACCTCTATTCCA
6455703 TTT
1 TTT
6455706 TAGTAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTCATTTTATTAAACCTCTATTCCA
Found at i:6457846 original size:23 final size:23
Alignment explanation
Indices: 6457820--6457863 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6457810 TGTGAGAAAA
*
6457820 ATTAAATTTA-AACACATAAATAC
1 ATTAAATTAAGAACAC-TAAATAC
*
6457843 ATTAGATTAAGAACACTAAAT
1 ATTAAATTAAGAACACTAAAT
6457864 GAGCACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (23 bp):
ATTAAATTAAGAACACTAAATAC
Found at i:6458505 original size:29 final size:31
Alignment explanation
Indices: 6458447--6458515 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
6458437 TATTTAAACC
* * *
6458447 AAATCAAAATTTCACGTGTATAATTGCACA-
1 AAATCAAAATTTCACGTATAAAATTACACAT
*
6458477 AAATCAAAATTT-ATGTATAAAATTACACATT
1 AAATCAAAATTTCACGTATAAAATTACACA-T
6458508 AAATCAAA
1 AAATCAAA
6458516 GTTCATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.39
30 12 0.36
31 8 0.24
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (31 bp):
AAATCAAAATTTCACGTATAAAATTACACAT
Found at i:6463941 original size:20 final size:21
Alignment explanation
Indices: 6463912--6463951 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6463902 GAATCCTTCT
*
6463912 TTTTTCCTCTTATTTTCTCTA
1 TTTTTCCTCTGATTTTCTCTA
6463933 TTTTT-CTCTGATTTTCTCT
1 TTTTTCCTCTGATTTTCTCT
6463952 CGATTTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTTCCTCTGATTTTCTCTA
Found at i:6464975 original size:219 final size:219
Alignment explanation
Indices: 6464596--6465150 Score: 941
Period size: 219 Copynumber: 2.5 Consensus size: 219
6464586 ATGCGATCTG
* * *
6464596 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTGTAATACGCTCCACTACAACTTCAGGGAG
1 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGAAG
* * *
6464661 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAAATTTAGGGAGATAAGATTGGTCATTTTCGAT
66 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCGAT
*
6464726 CTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTATAACTTCAG
131 CTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTATAACTTCAA
6464791 GGAGATAAGACCTGATGTGATCCA
196 GGAGATAAGACCTGATGTGATCCA
6464815 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGAAG
1 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGAAG
* *
6464880 ATAGGATCATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAAATAAGATTGGTCATCTTCGAT
66 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCGAT
*
6464945 CTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTGTAACTTCAA
131 CTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTATAACTTCAA
6465010 GGAGATAAGACCTGATGTGATCCA
196 GGAGATAAGACCTGATGTGATCCA
*
6465034 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCTGCTCCACTACAACTTCA-GAGA
1 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGA-A
* * * * * *
6465098 GATAGAATTATTGACTTCAATCTGCTCCACTGCAACCTCAAGGAGATAAGATT
65 GATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATT
6465151 TGCTTCTTCA
Statistics
Matches: 316, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
218 2 0.01
219 314 0.99
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (219 bp):
CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGAAG
ATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCGAT
CTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTATAACTTCAA
GGAGATAAGACCTGATGTGATCCA
Found at i:6465160 original size:44 final size:45
Alignment explanation
Indices: 6464591--6465149 Score: 307
Period size: 44 Copynumber: 12.7 Consensus size: 45
6464581 TCTTGATGCG
*
6464591 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-ATTACTGT-A
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTACT-TCA
* * * **
6464635 ATAC-GCTCCACTACAACTTCAGGGAGATAGGAT-T-ATCGGCTTCA
1 AT-CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGAT-TACTTCA
* * * * * * * *
6464679 ATCTGCTCCACTGTAAATTTAGGGAGATAAGAT-TGGTCATTTTCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTA-CTTCA
* * * * *
6464724 ATCTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG-AGAGATAAGATCTGATTACTTCA
* ** * * *
6464769 GTCTGCTCCACTATAACTTCAGGGAGATAAGACCTGATGTGA--TCC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGAT-T-ACTTCA
*
6464814 A-CT-CT--ACTGCAACTTCAGAGAGATAAGATCT-ATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTACTTCA
* * * **
6464854 ATCCGCTCCACTACAACTTCAG-GAAGATAGGATC--ATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGAT-TACTTCA
* * * * * *
6464898 ATCTGCTCCACTGTAACTTCAGGGAAATAAGAT-TGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTA-CTTCA
* * * * *
6464943 ATCTGCCCCACTGCAACTTCAGTCGGGATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG-AGAGATAAGATCTGATTACTTCA
* * * *
6464988 GTCTGCTCCACTGTAACTTCA-AGGAGATAAGACCTGATGTGA--TCC
1 ATCTGCTCCACTGCAACTTCAGA-GAGATAAGATCTGAT-T-ACTTCA
*
6465033 A-CT-CT--ACTGCAACTTCAGAGAGATAAGATCT-ATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTACTTCA
*
6465073 ATCTGCTCCACTACAACTTCAGAGAGAT-AGAAT-T-ATTGACTTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAG-ATCTGATT-ACTTCA
*
6465117 ATCTGCTCCACTGCAACCTCA-AGGAGATAAGAT
1 ATCTGCTCCACTGCAACTTCAGA-GAGATAAGAT
6465150 TTGCTTCTTC
Statistics
Matches: 393, Mismatches: 82, Indels: 80
0.71 0.15 0.14
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 8 0.02
41 47 0.12
42 5 0.01
43 19 0.05
44 191 0.49
45 89 0.23
46 22 0.06
47 8 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGATTACTTCA
Found at i:6465348 original size:87 final size:87
Alignment explanation
Indices: 6465223--6465407 Score: 255
Period size: 87 Copynumber: 2.1 Consensus size: 87
6465213 CCTTACACTT
* * * **
6465223 AAAGATAAGATTCGTCGTCTTCGATCTGTTTCCCTACTCCTGAGGAAGTTAAGATCCGTAATCTT
1 AAAGATAAGATTCGCCGTCTTAGATCTGTTTCCCTACTCCTGAGGAAGATAAGATCCACAA-CTT
*
6465288 CGATCTGTTTCCCTACTCCTGGG
65 AGATCTGTTTCCCTACTCCTGGG
* * * *
6465311 GAAGATAAGATTCGCCG-CTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCACTTA
1 AAAGATAAGATTCGCCGTCTTAGATCTGTTTCCCTACTCCTGAGGAAGATAAGATCCACAACTTA
*
6465375 GATCTGTTTCCCTACTCTTGGG
66 GATCTGTTTCCCTACTCCTGGG
6465397 AAAGATAAGAT
1 AAAGATAAGAT
6465408 CCGCAATATT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 34 0.40
87 36 0.42
88 15 0.18
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (87 bp):
AAAGATAAGATTCGCCGTCTTAGATCTGTTTCCCTACTCCTGAGGAAGATAAGATCCACAACTTA
GATCTGTTTCCCTACTCCTGGG
Found at i:6465350 original size:43 final size:43
Alignment explanation
Indices: 6465224--6465407 Score: 233
Period size: 43 Copynumber: 4.2 Consensus size: 43
6465214 CTTACACTTA
* * *
6465224 AAGATAAGATTCGTCGTCTTCGATCTGTTTCCCTACTCCTGAGG
1 AAGATAAGATTCGCCG-CTTAGATCTGTTTCCCTACTCCTGGGG
* * *** *
6465268 AAGTTAAGATCCGTAATCTTCGATCTGTTTCCCTACTCCTGGGG
1 AAGATAAGATTCG-CCGCTTAGATCTGTTTCCCTACTCCTGGGG
6465312 AAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGG
1 AAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGG
* * * *
6465355 AAGATAAGATTCACCACTTAGATCTGTTTCCCTACTCTTGGGA
1 AAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGG
6465398 AAGATAAGAT
1 AAGATAAGAT
6465408 CCGCAATATT
Statistics
Matches: 123, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
43 75 0.61
44 48 0.39
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (43 bp):
AAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGG
Found at i:6466631 original size:7 final size:7
Alignment explanation
Indices: 6466619--6466666 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
6466609 TAGCCTCTCT
6466619 ATTTTTC
1 ATTTTTC
6466626 ATTTTTC
1 ATTTTTC
6466633 A-TTTTC
1 ATTTTTC
6466639 ATTTTTC
1 ATTTTTC
*
6466646 A-TTCTC
1 ATTTTTC
6466652 ATTTTCATC
1 ATTTT--TC
6466661 ATTTTT
1 ATTTTT
6466667 TTACTCAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 11 0.31
7 17 0.49
9 7 0.20
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (7 bp):
ATTTTTC
Found at i:6466637 original size:6 final size:6
Alignment explanation
Indices: 6466621--6466659 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
6466611 GCCTCTCTAT
*
6466621 TTTTCA TTTTTCA TTTTCA TTTTTCA TTCTCA TTTTCA T
1 TTTTCA -TTTTCA TTTTCA -TTTTCA TTTTCA TTTTCA T
6466660 CATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTCA
Found at i:6466639 original size:13 final size:13
Alignment explanation
Indices: 6466621--6466656 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
6466611 GCCTCTCTAT
6466621 TTTTCATTTTTCA
1 TTTTCATTTTTCA
6466634 TTTTCATTTTTCA
1 TTTTCATTTTTCA
*
6466647 TTCTCATTTT
1 TTTTCATTTT
6466657 CATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:6467634 original size:23 final size:22
Alignment explanation
Indices: 6467602--6467672 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 22
6467592 TTGATCTTGA
*
6467602 TTTTGATTTTTTCTTATTTCTTCT
1 TTTTGATTTTTT-TTATTT-TTAT
*
6467626 TTTTGTTTTTTTTTTATTTTTAT
1 TTTTG-ATTTTTTTTATTTTTAT
*
6467649 TTTTGA-TTTTTTTATTTTCAT
1 TTTTGATTTTTTTTATTTTTAT
6467670 TTT
1 TTT
6467673 GCATTTGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 17 0.40
23 8 0.19
24 11 0.26
25 6 0.14
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTGATTTTTTTTATTTTTAT
Found at i:6467661 original size:24 final size:25
Alignment explanation
Indices: 6467602--6467661 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
6467592 TTGATCTTGA
*
6467602 TTTTGA-TTTTTTCTTATTTCTTCT
1 TTTTGATTTTTTTCTTATTTCTTAT
*
6467626 TTTTG-TTTTTTTTTTATTT-TTAT
1 TTTTGATTTTTTTCTTATTTCTTAT
6467649 TTTTGATTTTTTT
1 TTTTGATTTTTTT
6467662 ATTTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (25 bp):
TTTTGATTTTTTTCTTATTTCTTAT
Found at i:6469418 original size:20 final size:20
Alignment explanation
Indices: 6469390--6469433 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6469380 CCTCGAATCC
* *
6469390 CTCTTTTTTCCTCTTATTTT
1 CTCTATTTTCCTCTGATTTT
*
6469410 CTCTATTTTTCTCTGATTTT
1 CTCTATTTTCCTCTGATTTT
6469430 CTCT
1 CTCT
6469434 CGATTTCTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.25, G:0.02, T:0.66
Consensus pattern (20 bp):
CTCTATTTTCCTCTGATTTT
Found at i:6472152 original size:33 final size:33
Alignment explanation
Indices: 6472115--6472181 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
6472105 TGGCAATGAG
*
6472115 ATAAAATAGGATTGTATTGAGTGGATAGATTTA
1 ATAAAATAGGATTGTATTGAGTGGACAGATTTA
6472148 ATAAAATAGGATTGTATTGAGTGGACAGATTTA
1 ATAAAATAGGATTGTATTGAGTGGACAGATTTA
6472181 A
1 A
6472182 CTCAAAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.34
Consensus pattern (33 bp):
ATAAAATAGGATTGTATTGAGTGGACAGATTTA
Found at i:6472627 original size:19 final size:18
Alignment explanation
Indices: 6472591--6472641 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
6472581 GATTTTTGGA
*
6472591 AAAATTAAATTTGACAAAT
1 AAAATTAAA-TTAACAAAT
6472610 AAAATTAAATTAATCAAAT
1 AAAATTAAATTAA-CAAAT
6472629 -AAATTAAAATTAA
1 AAAATT-AAATTAA
6472642 AAAGATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATTAAATTAACAAAT
Found at i:6473631 original size:14 final size:14
Alignment explanation
Indices: 6473608--6473643 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6473598 TTTCACTGCA
*
6473608 TTTTCTAAACCTAT
1 TTTTCCAAACCTAT
*
6473622 TTTTCCAAACCTGT
1 TTTTCCAAACCTAT
6473636 TTTTCCAA
1 TTTTCCAA
6473644 CAGATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTCCAAACCTAT
Found at i:6480540 original size:44 final size:44
Alignment explanation
Indices: 6480477--6480567 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
6480467 AACTCTGTTT
6480477 TTAGTTTCTCACTTAAACTCTTATTAGTGTAAGTTATTTTAATA
1 TTAGTTTCTCACTTAAACTCTTATTAGTGTAAGTTATTTTAATA
* *
6480521 TTAGTTTC-CTACTTAAACTCTTATTGGTGTAGGTTATTTTAATA
1 TTAGTTTCTC-ACTTAAACTCTTATTAGTGTAAGTTATTTTAATA
6480565 TTA
1 TTA
6480568 TTTGACCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (44 bp):
TTAGTTTCTCACTTAAACTCTTATTAGTGTAAGTTATTTTAATA
Found at i:6490818 original size:5 final size:5
Alignment explanation
Indices: 6490810--6490835 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6490800 GAGATGGAAT
6490810 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
6490836 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:6490835 original size:26 final size:26
Alignment explanation
Indices: 6490784--6490835 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
6490774 TGAAGTTTTC
* * *
6490784 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
6490810 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
6490836 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:6491383 original size:17 final size:17
Alignment explanation
Indices: 6491356--6491401 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
6491346 AAAGTTTAGG
6491356 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
6491374 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
6491389 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
6491402 TAAGGGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:6496164 original size:22 final size:24
Alignment explanation
Indices: 6496138--6496181 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
6496128 GAAAAATATT
6496138 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
6496160 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
6496182 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:6496289 original size:9 final size:9
Alignment explanation
Indices: 6496275--6496302 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6496265 TTTTGTTACA
6496275 ACAATTAAT
1 ACAATTAAT
6496284 ACAATTAAT
1 ACAATTAAT
6496293 ACAATTAAT
1 ACAATTAAT
6496302 A
1 A
6496303 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6496318 original size:68 final size:66
Alignment explanation
Indices: 6496245--6496386 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
6496235 TCAAGTTTGT
*
6496245 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
6496310 AAA
64 AAA
*
6496313 TTTACTAATCAAATGTTAGATTTTATTACAGCAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
6496378 T
66 A
6496379 TTTACTAA
1 TTTACTAA
6496387 CAATTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 43 0.61
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:6496396 original size:16 final size:16
Alignment explanation
Indices: 6496375--6496416 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6496365 AATAATTTGA
*
6496375 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
6496391 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
6496407 TAGTTTTAAT
1 TAATTTTAAT
6496417 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:6496400 original size:22 final size:23
Alignment explanation
Indices: 6496390--6496452 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
6496380 TTACTAACAA
* * *
6496390 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
6496412 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
6496435 TTAATTTTA-ATTAAAAAT
1 TTAATTTTATATAAAAAAT
6496453 GGGCCGGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:6496407 original size:59 final size:65
Alignment explanation
Indices: 6496245--6496408 Score: 196
Period size: 68 Copynumber: 2.5 Consensus size: 65
6496235 TCAAGTTTGT
* *
6496245 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGA-TTT-TAATAACAATTAATACAATTAATACAATTAATAATTTGAT
6496310 AAA
63 AAA
*
6496313 TTTACTAATCAAATGTTAGATTTTATTACAGCAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTAATA-A-CAATTAATACAATTAATACAATTAATAATTTGAT
*
6496376 AAT
63 AAA
6496379 TTTACTAA-C-AA-TTA-ATTTTAATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTAATAACAATTA
6496409 GTTTTAATTT
Statistics
Matches: 89, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
59 6 0.07
60 1 0.01
61 8 0.09
62 3 0.03
64 2 0.02
65 1 0.01
66 29 0.33
67 5 0.06
68 34 0.38
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (65 bp):
TTTACTAATCAAAGTTAGATTTTAATAACAATTAATACAATTAATACAATTAATAATTTGATAAA
Found at i:6500046 original size:23 final size:23
Alignment explanation
Indices: 6500004--6500047 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6499994 AGCTCTCTAT
*
6500004 ATATAAACAAGAAGGAAAGAAAG
1 ATATAAACAAGAAGAAAAGAAAG
6500027 ATATAAA-AAGAAGAAGAAGAA
1 ATATAAACAAGAAGAA-AAGAA
6500048 GAAGAAGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.09
Consensus pattern (23 bp):
ATATAAACAAGAAGAAAAGAAAG
Found at i:6500052 original size:25 final size:25
Alignment explanation
Indices: 6500002--6500050 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
6499992 TCAGCTCTCT
* *
6500002 ATATATAAACAAGAAGGAAAGAAAG
1 ATATAAAAACAAGAAGAAAAGAAAG
*
6500027 ATATAAAAAGAAGAAGAAGAAGAA
1 ATATAAAAACAAGAAGAA-AAGAA
6500051 GAAGGCGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.10
Consensus pattern (25 bp):
ATATAAAAACAAGAAGAAAAGAAAG
Found at i:6518457 original size:289 final size:285
Alignment explanation
Indices: 6517926--6518713 Score: 789
Period size: 289 Copynumber: 2.7 Consensus size: 285
6517916 TCTTAAAAGA
* * * *
6517926 CTAGCCAAGTGGTAGTGTACTTATCCACTAATGCCATTTAAGGGCATAGATTCAAACCCCACCAA
1 CTAGCCAAATGGTAGTGTTCTTAACCACTAATGCCATTTAAGGGCATAG-TTCGAA-CCCACCAA
* * * * * *
6517991 GACCAAGTGCTAAACATTTCCTTGGTGGTAAGGCGCTCTCCAAACTCTATGAACATTGGGCTCTG
64 G-CCAAATGCT-AACATTTCCTTGGTGGTGAGGCGTTC-CCAAACTCCATGAACCTTGGGCTCTC
* * * * * * * *
6518056 CTCAAAGTCGAGAGATAAAACCTAAGGCTAAAACCAAGCATAAACACCCCAGACACAATACCTCT
126 CTCGAAGTCGAGAGAAAAAACTTAAGGCTAAAACCGAGCATAGATA-CTCAGACACAATACCTCC
* ** * *
6518121 ATTGTTGAGGGGTT-TGTCGGCTCCCTGAATGACACTCCAAAAAGATGTCTCCCAGAGCGAGACC
190 ATCGTTGAGGGGTTCAATCGGCTCCCTGAACGACACTCCAAAAAGATGTCTCCCAAAGCGAGACC
* * **
6518185 GATCTC-CCCTTAACAAAAAATGCACTTTTTTT
255 GACCTCTCCCTCAACAAAAAA--CACCCTTTTT
*
6518217 CTAGCCAAATGGTAGTGTTCTTAACCACTAATGCCATTTAAGGGCAT-GTTCGAACGCCACAAAT
1 CTAGCCAAATGGTAGTGTTCTTAACCACTAATGCCATTTAAGGGCATAGTTCGAAC-CCACCAA-
* *
6518281 GTCAAATGCTAACATTTCCTTAGTGGTGAGGCGTTCCACAAACTCCATGAATCCTTGGGCTCTCC
64 GCCAAATGCTAACATTTCCTTGGTGGTGAGGCGTTCC-CAAACTCCATGAA-CCTTGGGCTCTCC
* * * * * *
6518346 TCGGAGTTGAGAGAAAAAACTTAAGGCTAGAACCGAGCATAGATATCTCAGGCACAAAACATCCA
127 TCGAAGTCGAGAGAAAAAACTTAAGGCTAAAACCGAGCATAGATA-CTCAGACACAATACCTCCA
* * * * *
6518411 CCGTTGAGGGGTTCAAT-GGCTCCCT-AGACGACATTCCTAGAAGATGTCTCCCAAAGCGAGACT
191 TCGTTGAGGGGTTCAATCGGCTCCCTGA-ACGACACTCCAAAAAGATGTCTCCCAAAGCGAGACC
6518474 GACCTCTCCCTCAACAAAAAACACCCTTTTT
255 GACCTCTCCCTCAACAAAAAACACCCTTTTT
* * * * * * * *
6518505 CTAGACAACTAGTAGTGTTCTTAGCCATTAATGTCATTTATGGGCATGAGTTTGAACCCTACCAA
1 CTAGCCAAATGGTAGTGTTCTTAACCACTAATGCCATTTAAGGGCAT-AGTTCGAACCC-ACCAA
* * **
6518570 GGCCAAATGTTAATATTTCCTTGGTGGTGA-GCTGTTATGCAAACTCCATGAACCTTTGGGCTCT
64 -GCCAAATGCTAACATTTCCTTGGTGGTGAGGC-GTT-CCCAAACTCCATGAACC-TTGGGCTCT
* * * * * * *
6518634 CATCGAAATCGAAAGACAAAACTCAA-GCTAAAACTGAGTATAGATACTCTAGACACAATACCTC
125 CCTCGAAGTCGAGAGAAAAAACTTAAGGCTAAAACCGAGCATAGATACTC-AGACACAATACCTC
*
6518698 CATCATTGAGGGGTTC
189 CATCGTTGAGGGGTTC
6518714 GCTAACTCCT
Statistics
Matches: 410, Mismatches: 73, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
287 1 0.00
288 88 0.21
289 181 0.44
290 96 0.23
291 44 0.11
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (285 bp):
CTAGCCAAATGGTAGTGTTCTTAACCACTAATGCCATTTAAGGGCATAGTTCGAACCCACCAAGC
CAAATGCTAACATTTCCTTGGTGGTGAGGCGTTCCCAAACTCCATGAACCTTGGGCTCTCCTCGA
AGTCGAGAGAAAAAACTTAAGGCTAAAACCGAGCATAGATACTCAGACACAATACCTCCATCGTT
GAGGGGTTCAATCGGCTCCCTGAACGACACTCCAAAAAGATGTCTCCCAAAGCGAGACCGACCTC
TCCCTCAACAAAAAACACCCTTTTT
Found at i:6518809 original size:23 final size:23
Alignment explanation
Indices: 6518779--6518823 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6518769 TCAACAGATT
*
6518779 TGAAGTTCAAATTTTAGCATCTG
1 TGAAGTTCAAATTTTAACATCTG
* *
6518802 TGAAGTTCGAGTTTTAACATCT
1 TGAAGTTCAAATTTTAACATCT
6518824 ATAATCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
TGAAGTTCAAATTTTAACATCTG
Found at i:6520674 original size:12 final size:11
Alignment explanation
Indices: 6520637--6520698 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 11
6520627 TTTAGCAATT
*
6520637 TTATTATTTAGA
1 TTATTATTT-TA
*
6520649 TAATTATTTTA
1 TTATTATTTTA
6520660 TTATTATTTTCA
1 TTATTATTTT-A
6520672 TTATTATTAATTA
1 TTATTATT--TTA
6520685 TTATTAGTTTTA
1 TTATTA-TTTTA
6520697 TT
1 TT
6520699 TTCCTTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
11 10 0.23
12 22 0.51
13 7 0.16
14 4 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:6520675 original size:15 final size:15
Alignment explanation
Indices: 6520657--6520714 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
6520647 GATAATTATT
6520657 TTATTATTATTTTCA
1 TTATTATTATTTTCA
6520672 TTATTATTAATTATT-A
1 TTATTATT-ATT-TTCA
*
6520688 TTAGTT-TTATTTTCC
1 TTA-TTATTATTTTCA
6520703 TT-TTATTTATTT
1 TTATTA-TTATTT
6520715 GTGACTATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 19 0.53
16 9 0.25
17 4 0.11
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTATTATTTTCA
Found at i:6520685 original size:30 final size:30
Alignment explanation
Indices: 6520649--6520709 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
6520639 ATTATTTAGA
6520649 TAATTATT-TTA-TTATTATTTTCATTATTAT
1 TAATTATTATTAGTT-TTATTTTCATT-TTAT
*
6520679 TAATTATTATTAGTTTTATTTTCCTTTTAT
1 TAATTATTATTAGTTTTATTTTCATTTTAT
6520709 T
1 T
6520710 TATTTGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 13 0.46
31 13 0.46
32 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (30 bp):
TAATTATTATTAGTTTTATTTTCATTTTAT
Found at i:6532010 original size:56 final size:56
Alignment explanation
Indices: 6531949--6532058 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
6531939 TTGTGCGTAG
*
6531949 GAGTATTGTCTTTATAGGTGTTTGCGTCATTACTTATTGATTGATTGTGGTAGTAA
1 GAGTATTGTCTTTATAGGTGTTTGCCTCATTACTTATTGATTGATTGTGGTAGTAA
*
6532005 GAGTATTGTCTTTGTAGGTGTTTGCCTCATTACTTATTGATTGATTGTGGTAGT
1 GAGTATTGTCTTTATAGGTGTTTGCCTCATTACTTATTGATTGATTGTGGTAGT
6532059 TCAGTTGGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.47
Consensus pattern (56 bp):
GAGTATTGTCTTTATAGGTGTTTGCCTCATTACTTATTGATTGATTGTGGTAGTAA
Found at i:6537354 original size:13 final size:13
Alignment explanation
Indices: 6537338--6537373 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
6537328 AATAGGGCTT
6537338 GTAAATATTTTTA
1 GTAAATATTTTTA
6537351 GTAAATATTTTTA
1 GTAAATATTTTTA
*
6537364 ATAAATATTT
1 GTAAATATTT
6537374 AGGAAGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
GTAAATATTTTTA
Found at i:6538667 original size:25 final size:25
Alignment explanation
Indices: 6538614--6538671 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
6538604 AAACTTTAGC
* * *
6538614 GTGCTCTCTGATTATTAGCTCGTTG
1 GTGCTCTCTGATTACTAGCTCGATA
6538639 GTGCTCTCTGATTACTAGCAT-GATA
1 GTGCTCTCTGATTACTAGC-TCGATA
6538664 GTGCTCTC
1 GTGCTCTC
6538672 CATTTAGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCTCGATA
Found at i:6538711 original size:22 final size:23
Alignment explanation
Indices: 6538662--6538716 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
6538652 ACTAGCATGA
*
6538662 TAGTGCTCTCCATTTAGCACATC
1 TAGTGCTCTCTATTTAGCACATC
* *
6538685 T-GTGCTCTCTTTTTAGCAC-TT
1 TAGTGCTCTCTATTTAGCACATC
6538706 TAGTGCTCTCT
1 TAGTGCTCTCT
6538717 GTTCATTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.89
23 1 0.04
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.44
Consensus pattern (23 bp):
TAGTGCTCTCTATTTAGCACATC
Found at i:6543204 original size:13 final size:13
Alignment explanation
Indices: 6543186--6543220 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6543176 CAATTTTCTT
*
6543186 TTATTATTATTAA
1 TTATTATTAATAA
*
6543199 TTATTAATAATAA
1 TTATTATTAATAA
6543212 TTATTATTA
1 TTATTATTA
6543221 CATTCAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTAATAA
Found at i:6544777 original size:16 final size:18
Alignment explanation
Indices: 6544756--6544790 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6544746 GTTCCCATTG
6544756 TTTTCC-TCT-TTTTTTT
1 TTTTCCTTCTATTTTTTT
6544772 TTTTCCTTCTATTTTTTT
1 TTTTCCTTCTATTTTTTT
6544790 T
1 T
6544791 CTTGATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCCTTCTATTTTTTT
Found at i:6544788 original size:17 final size:16
Alignment explanation
Indices: 6544756--6544790 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6544746 GTTCCCATTG
*
6544756 TTTTCCTCTTTTTTTT
1 TTTTCCTCTATTTTTT
6544772 TTTTCCTTCTATTTTTT
1 TTTTCC-TCTATTTTTT
6544789 TT
1 TT
6544791 CTTGATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCCTCTATTTTTT
Found at i:6551924 original size:3 final size:3
Alignment explanation
Indices: 6551910--6551950 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6551900 GGGTTTTTCA
6551910 CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6551951 TTATTTGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:6556374 original size:18 final size:19
Alignment explanation
Indices: 6556351--6556389 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6556341 TACAAATACA
*
6556351 AACATT-ACATAATTATTT
1 AACATTCACATAATAATTT
*
6556369 AACATTCACATCATAATTT
1 AACATTCACATAATAATTT
6556388 AA
1 AA
6556390 TCTCATCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATAATTT
Found at i:6556893 original size:31 final size:31
Alignment explanation
Indices: 6556858--6556916 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6556848 TTACAACATA
* *
6556858 TTTCATATTCTATTTTCAATTCACTATCGTT
1 TTTCACATTCTACTTTCAATTCACTATCGTT
6556889 TTTCACATTCTACTTTCAATTCACTATC
1 TTTCACATTCTACTTTCAATTCACTATC
6556917 TCATATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTCACATTCTACTTTCAATTCACTATCGTT
Found at i:6557035 original size:22 final size:22
Alignment explanation
Indices: 6557007--6557085 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
6556997 GCACTAATGA
6557007 ACAGAGAGCACTGAAGTGCTAT
1 ACAGAGAGCACTGAAGTGCTAT
* *
6557029 ACAGAGAGCACTGAAGTACTAA
1 ACAGAGAGCACTGAAGTGCTAT
* *
6557051 ACGGAGAGCACTGACGTGCTAAT
1 ACAGAGAGCACTGAAGTGCT-AT
6557074 AATCAGAGAGCA
1 -A-CAGAGAGCA
6557086 TTGGCGTGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 37 0.79
23 1 0.02
24 1 0.02
25 8 0.17
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (22 bp):
ACAGAGAGCACTGAAGTGCTAT
Found at i:6557093 original size:25 final size:25
Alignment explanation
Indices: 6557000--6557176 Score: 179
Period size: 25 Copynumber: 7.3 Consensus size: 25
6556990 TTATTATGCA
*
6557000 CTAATGAA-CAGAGAGCACTGAAGTG
1 CTAAT-AATCAGAGAGCACTGACGTG
* *
6557025 CT-AT-A-CAGAGAGCACTGAAGTA
1 CTAATAATCAGAGAGCACTGACGTG
*
6557047 CT-A-AA-CGGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
* *
6557069 CTAATAATCAGAGAGCATTGGCGTG
1 CTAATAATCAGAGAGCACTGACGTG
* *
6557094 CTAATAATTAGAGAGCACTGGCGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
6557119 CTAATAATCGGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
* ** *
6557144 ATAATAATTGGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
6557169 CTAATAAT
1 CTAATAAT
6557177 TAAAGAGCGC
Statistics
Matches: 132, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
22 37 0.28
23 1 0.01
24 4 0.03
25 90 0.68
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:6560743 original size:34 final size:34
Alignment explanation
Indices: 6560700--6560767 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6560690 TTATTTGGAA
6560700 ATGGCTCATTAGGAGTTCAAGCGCAAGCTTGGGT
1 ATGGCTCATTAGGAGTTCAAGCGCAAGCTTGGGT
6560734 ATGGCTCATTAGGAGTTCAAGCGCAAGCTTGGGT
1 ATGGCTCATTAGGAGTTCAAGCGCAAGCTTGGGT
6560768 CTTTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (34 bp):
ATGGCTCATTAGGAGTTCAAGCGCAAGCTTGGGT
Found at i:6561499 original size:26 final size:27
Alignment explanation
Indices: 6561454--6561510 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
6561444 AAATCCCAAA
* *
6561454 TTTTCTTTCTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTTCCTCCCCTGTTTTCG
6561480 TTTTCTTTCCTTT-CTCCCCTGTTTTCG
1 TTTTCTTT-CTTTCCTCCCCTGTTTTCG
6561507 TTTT
1 TTTT
6561511 GCTATTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTCTTTCTTTCCTCCCCTGTTTTCG
Found at i:6563376 original size:21 final size:21
Alignment explanation
Indices: 6563348--6563411 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
6563338 TTTGGGTGGA
6563348 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
*
6563369 TTAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
*
6563390 TCAGCTCTCACGAGCTTTTGT
1 TCAGCTCTCACGAGCTTCTGT
6563411 T
1 T
6563412 GGCGTGTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.38
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:6563650 original size:18 final size:17
Alignment explanation
Indices: 6563629--6563672 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
6563619 ATGATGGTAC
6563629 ATGATATATTGATATAT-A
1 ATGATATATTGA-A-ATGA
6563647 ATGATATATTGAAATGA
1 ATGATATATTGAAATGA
6563664 ATGATATAT
1 ATGATATAT
6563673 GTATATGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 11 0.44
18 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (17 bp):
ATGATATATTGAAATGA
Found at i:6563680 original size:17 final size:17
Alignment explanation
Indices: 6563629--6563681 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
6563619 ATGATGGTAC
6563629 ATGATATATTGATATAT-A
1 ATGATATA-TG-TATATGA
*
6563647 ATGATATAT-TGAAATGA
1 ATGATATATGT-ATATGA
6563664 ATGATATATGTATATGA
1 ATGATATATGTATATGA
6563681 A
1 A
6563682 GAAATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 17 0.57
18 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (17 bp):
ATGATATATGTATATGA
Found at i:6566057 original size:25 final size:25
Alignment explanation
Indices: 6566029--6566076 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
6566019 ATTTAGCCCG
6566029 GATCGAAGCTCATTAGAGTAATTCA
1 GATCGAAGCTCATTAGAGTAATTCA
6566054 GATCGAAGCTCATTAGAGTAATT
1 GATCGAAGCTCATTAGAGTAATT
6566077 GTCATTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (25 bp):
GATCGAAGCTCATTAGAGTAATTCA
Found at i:6568659 original size:26 final size:26
Alignment explanation
Indices: 6568630--6568685 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
6568620 ATTTAGAGAT
*
6568630 AAAATAGGCCAATGTGTGACATAAGG
1 AAAATAGGCCAATGTGCGACATAAGG
*
6568656 AAAATGGGCCAATGTGCGACATAAGG
1 AAAATAGGCCAATGTGCGACATAAGG
6568682 AAAA
1 AAAA
6568686 GTTGGTGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.27, T:0.16
Consensus pattern (26 bp):
AAAATAGGCCAATGTGCGACATAAGG
Found at i:6568792 original size:15 final size:15
Alignment explanation
Indices: 6568767--6568801 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6568757 GACTCTATTT
*
6568767 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
6568781 TAATTAATATTAAGA
1 TAATTAATATTAAGA
6568796 TAATTA
1 TAATTA
6568802 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:6570808 original size:30 final size:30
Alignment explanation
Indices: 6570772--6570829 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
6570762 AATAATAATG
6570772 CATTGATACTAATGTGTAGTTGGTTGATAA
1 CATTGATACTAATGTGTAGTTGGTTGATAA
6570802 CATTGATACTAATGTGTAGTTGGTTGAT
1 CATTGATACTAATGTGTAGTTGGTTGAT
6570830 GACAAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (30 bp):
CATTGATACTAATGTGTAGTTGGTTGATAA
Found at i:6573377 original size:18 final size:18
Alignment explanation
Indices: 6573354--6573389 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6573344 CAACTTAGCC
6573354 CGAGCCTCACCCTCACCA
1 CGAGCCTCACCCTCACCA
6573372 CGAGCCTCACCCTCACCA
1 CGAGCCTCACCCTCACCA
6573390 TACTCTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.56, G:0.11, T:0.11
Consensus pattern (18 bp):
CGAGCCTCACCCTCACCA
Found at i:6591483 original size:220 final size:220
Alignment explanation
Indices: 6591101--6591539 Score: 815
Period size: 220 Copynumber: 2.0 Consensus size: 220
6591091 AACATAATTT
6591101 TAATCACACATAAATTTCATTGTTTGTTCAATTTCCAGCAAGCTATTTTTCTGCGTCACGGTCAC
1 TAATCACACATAAATTTCATTGTTTGTTCAATTTCCAGCAAGCTATTTTTCTGCGTCACGGTCAC
6591166 TAATTTATATTTATCTGGAGCTACAGGGCTCCAAATTGAGTTCCGTAAATTTTACCCGAAACTAG
66 TAATTTATATTTATCTGGAGCTACAGGGCTCCAAATTGAGTTCCGTAAATTTTACCCGAAACTAG
6591231 ATTCATACACCTTTCCACCATAAAATTTTCAGAAGTTTTGATTTGGCAAATTAGTACAGTTTATT
131 ATTCATACACCTTTCCACCATAAAATTTTCAGAAGTTTTGATTTGGCAAATTAGTACAGTTTATT
6591296 CTCTAAAGATTCCCCTGTTTCACTA
196 CTCTAAAGATTCCCCTGTTTCACTA
* * *
6591321 TAATCACACATAAATTTCATTGTTTGTTCCATTTCCAGCAATCTGTTTTTCTGCGTCACGGTCAC
1 TAATCACACATAAATTTCATTGTTTGTTCAATTTCCAGCAAGCTATTTTTCTGCGTCACGGTCAC
*
6591386 TAATTTATATTTATCTGGAGCTACGGGGCTCCAAATTGAGTTCCGTAAATTTTACCCGAAACTAG
66 TAATTTATATTTATCTGGAGCTACAGGGCTCCAAATTGAGTTCCGTAAATTTTACCCGAAACTAG
* *
6591451 ATTCATATACCTTTCCACCATAAAATTTTCAGAAGTTTTGGTTTGGCAAATTAGTACAGTTTATT
131 ATTCATACACCTTTCCACCATAAAATTTTCAGAAGTTTTGATTTGGCAAATTAGTACAGTTTATT
*
6591516 CTCTAAAGATTCTCCTGTTTCACT
196 CTCTAAAGATTCCCCTGTTTCACT
6591540 GCTCGACAGT
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 212 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (220 bp):
TAATCACACATAAATTTCATTGTTTGTTCAATTTCCAGCAAGCTATTTTTCTGCGTCACGGTCAC
TAATTTATATTTATCTGGAGCTACAGGGCTCCAAATTGAGTTCCGTAAATTTTACCCGAAACTAG
ATTCATACACCTTTCCACCATAAAATTTTCAGAAGTTTTGATTTGGCAAATTAGTACAGTTTATT
CTCTAAAGATTCCCCTGTTTCACTA
Found at i:6592079 original size:33 final size:33
Alignment explanation
Indices: 6592037--6592291 Score: 164
Period size: 33 Copynumber: 7.4 Consensus size: 33
6592027 GTGGATTCAA
*
6592037 CACTTAGCAACCACCAATGAGTCGAGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
* * *
6592070 CACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAG
1 CACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAATCAG
* *
6592112 CACTTAGCAACCACCAATAATTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
*
6592145 CACTTAGCAACC-CC------TCGGGGTAATCAA
1 CACTTAGCAACCACCAATGAGTCGGGG-AATCAG
6592172 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
* * *
6592205 CACTTAACAACCCCTTTCACATTTAAGATACGGTGGAATCAG
1 CACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAATCAG
* * **
6592247 CACATAGCAACCACCAATGAATCGGAAAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
6592280 CACTTAGCAACC
1 CACTTAGCAACC
6592292 CCTTGGGGGA
Statistics
Matches: 176, Mismatches: 20, Indels: 52
0.71 0.08 0.21
Matches are distributed among these distances:
26 6 0.03
27 17 0.10
28 2 0.01
32 2 0.01
33 66 0.38
34 12 0.07
35 2 0.01
36 9 0.05
37 2 0.01
38 2 0.01
39 10 0.06
40 2 0.01
41 5 0.03
42 39 0.22
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (33 bp):
CACTTAGCAACCACCAATGAGTCGGGGAATCAG
Found at i:6592175 original size:27 final size:26
Alignment explanation
Indices: 6592133--6592183 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
6592123 CACCAATAAT
*
6592133 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
6592159 TCGGGGTAATCAACACTTAGCAACC
1 TCGGGG-AATCAACACTTAGCAACC
6592184 ACCAATGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (26 bp):
TCGGGGAATCAACACTTAGCAACCCC
Found at i:6592205 original size:60 final size:60
Alignment explanation
Indices: 6592107--6592219 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
6592097 ATACGGTGGG
* * *
6592107 ATCAGCACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCGGGGTA
1 ATCAACACTTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAACAACCCCTCGGGGTA
*
6592167 ATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAACAACCCCT
1 ATCAACACTTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAACAACCCCT
6592220 TTCACATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.18
Consensus pattern (60 bp):
ATCAACACTTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAACAACCCCTCGGGGTA
Found at i:6592278 original size:135 final size:135
Alignment explanation
Indices: 6592024--6592318 Score: 466
Period size: 135 Copynumber: 2.2 Consensus size: 135
6592014 TTATCCGTTA
* * *
6592024 TCGGTGGATTCAACACTTAGCAACCACCAATGAGTCGAGGAATCAGCACTTAGCAACCCCTTTCA
1 TCGGGGGAATCAACACTTAGCAACCACCAATGAGTCGAGGAATCAGCACTTAACAACCCCTTTCA
* * **
6592089 CATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCA
66 CATTTAAGATACGGTGGAATCAGCACATAGCAACCACCAATAATTCGGAAAATCAGCACTTAGCA
6592154 ACCCC
131 ACCCC
* *
6592159 TCGGGGTAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAACAACCCCTTTCA
1 TCGGGGGAATCAACACTTAGCAACCACCAATGAGTCGAGGAATCAGCACTTAACAACCCCTTTCA
6592224 CATTTAAGATACGGTGGAATCAGCACATAGCAACCACCAATGAA-TCGGAAAATCAGCACTTAGC
66 CATTTAAGATACGGTGGAATCAGCACATAGCAACCACCAAT-AATTCGGAAAATCAGCACTTAGC
6592288 AACCCC
130 AACCCC
* * *
6592294 TTGGGGGAATTAGCACTTAGCAACC
1 TCGGGGGAATCAACACTTAGCAACC
6592319 CCCTTTATAT
Statistics
Matches: 146, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
135 144 0.99
136 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (135 bp):
TCGGGGGAATCAACACTTAGCAACCACCAATGAGTCGAGGAATCAGCACTTAACAACCCCTTTCA
CATTTAAGATACGGTGGAATCAGCACATAGCAACCACCAATAATTCGGAAAATCAGCACTTAGCA
ACCCC
Found at i:6595736 original size:104 final size:105
Alignment explanation
Indices: 6595486--6595753 Score: 459
Period size: 105 Copynumber: 2.6 Consensus size: 105
6595476 TAACCGTTAT
* *
6595486 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
6595551 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
6595591 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
6595655 GAATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
6595695 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
6595754 TTTATATACA
Statistics
Matches: 154, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
104 71 0.46
105 83 0.54
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:6596113 original size:29 final size:29
Alignment explanation
Indices: 6596080--6596143 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6596070 TAATCCACCA
6596080 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
6596109 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
6596139 CCCAA
1 CCCAA
6596144 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:6596117 original size:30 final size:30
Alignment explanation
Indices: 6596087--6596143 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6596077 CCACCCAACT
6596087 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
6596116 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
6596144 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:6603136 original size:26 final size:26
Alignment explanation
Indices: 6603106--6603156 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
6603096 ACCAATGAAC
*
6603106 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
6603132 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
6603157 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:6603204 original size:103 final size:105
Alignment explanation
Indices: 6602968--6603234 Score: 450
Period size: 103 Copynumber: 2.6 Consensus size: 105
6602958 TAACCGTTAT
* *
6602968 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
6603033 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
6603073 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
6603136 GAATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
6603176 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
6603235 TTTATATACA
Statistics
Matches: 153, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
103 71 0.46
104 26 0.17
105 56 0.37
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (105 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:6603596 original size:29 final size:29
Alignment explanation
Indices: 6603563--6603626 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6603553 TAATCCACCA
6603563 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
6603592 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
6603622 CCCAA
1 CCCAA
6603627 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:6603600 original size:30 final size:30
Alignment explanation
Indices: 6603570--6603626 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6603560 CCACCCAACT
6603570 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
6603599 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
6603627 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:6605488 original size:20 final size:20
Alignment explanation
Indices: 6605463--6605505 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
6605453 TTGTTAATGA
6605463 AAGATTAAGTTAATATAATT
1 AAGATTAAGTTAATATAATT
*
6605483 AAGATTAAGTTAATTTAATT
1 AAGATTAAGTTAATATAATT
6605503 AAG
1 AAG
6605506 TTGTTAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (20 bp):
AAGATTAAGTTAATATAATT
Found at i:6608380 original size:21 final size:22
Alignment explanation
Indices: 6608356--6608400 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
6608346 TTATAATTAT
*
6608356 TTTTAAGATGT-TTTATTAAAA
1 TTTTAAGATATATTTATTAAAA
*
6608377 TTTTAATATATATTTATTAAAA
1 TTTTAAGATATATTTATTAAAA
6608399 TT
1 TT
6608401 ATTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAAGATATATTTATTAAAA
Found at i:6608407 original size:22 final size:21
Alignment explanation
Indices: 6608367--6608411 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
6608357 TTTAAGATGT
6608367 TTTATTAAAATTTTAATATATA
1 TTTATTAAAATTTTAATAT-TA
6608389 TTTATTAAAATTATT-ATATTA
1 TTTATTAAAATT-TTAATATTA
6608410 TT
1 TT
6608412 GAAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATTAAAATTTTAATATTA
Found at i:6608416 original size:17 final size:18
Alignment explanation
Indices: 6608385--6608420 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6608375 AATTTTAATA
6608385 TATATTTATTAAAATTAT
1 TATATTTATTAAAATTAT
*
6608403 TATA-TTATTGAAATTAT
1 TATATTTATTAAAATTAT
6608420 T
1 T
6608421 TCTTTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATATTTATTAAAATTAT
Found at i:6609683 original size:28 final size:28
Alignment explanation
Indices: 6609643--6609702 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
6609633 ACAACACCAC
6609643 CAATAATAATAATAATAGCAGCCAGCTA
1 CAATAATAATAATAATAGCAGCCAGCTA
6609671 CAATAATAATAATAATAGCAGCCAGCTA
1 CAATAATAATAATAATAGCAGCCAGCTA
6609699 CAAT
1 CAAT
6609703 TATTGAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (28 bp):
CAATAATAATAATAATAGCAGCCAGCTA
Found at i:6613957 original size:18 final size:19
Alignment explanation
Indices: 6613917--6613958 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6613907 TTTATATCTA
6613917 AAAT-AAATAAATATATTT
1 AAATAAAATAAATATATTT
*
6613935 -CATAAAATAAA-ATATTT
1 AAATAAAATAAATATATTT
6613952 AAATAAA
1 AAATAAA
6613959 TAGTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAAATAAATATATTT
Found at i:6613959 original size:17 final size:18
Alignment explanation
Indices: 6613917--6613960 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
6613907 TTTATATCTA
6613917 AAATAAATAAATATATTT
1 AAATAAATAAATATATTT
*
6613935 -CATAAAATAAA-ATATTT
1 AAAT-AAATAAATATATTT
6613952 AAATAAATA
1 AAATAAATA
6613961 GTAAATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAATAAATATATTT
Found at i:6614590 original size:20 final size:20
Alignment explanation
Indices: 6614561--6614601 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6614551 ATATTACCAA
* *
6614561 TTCAGTTAATTTTGGTTAAT
1 TTCAGCTAATTTTAGTTAAT
6614581 TTCAGCTAATTTTAGTTAAT
1 TTCAGCTAATTTTAGTTAAT
6614601 T
1 T
6614602 CGGTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (20 bp):
TTCAGCTAATTTTAGTTAAT
Found at i:6615084 original size:21 final size:20
Alignment explanation
Indices: 6615047--6615087 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
6615037 TTTTACATAG
*
6615047 GGATTTTGTTTTAAAGTTTA
1 GGATTTTGGTTTAAAGTTTA
*
6615067 GGATTTTAGGTTTCAAGTTTA
1 GGATTTT-GGTTTAAAGTTTA
6615088 TATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (20 bp):
GGATTTTGGTTTAAAGTTTA
Found at i:6615753 original size:16 final size:17
Alignment explanation
Indices: 6615732--6615765 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6615722 AAACAAATAA
6615732 GAAATAA-TTTATCTTT
1 GAAATAAGTTTATCTTT
*
6615748 GAAATAAGTTTATTTTT
1 GAAATAAGTTTATCTTT
6615765 G
1 G
6615766 TGGTTAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
GAAATAAGTTTATCTTT
Found at i:6616424 original size:21 final size:21
Alignment explanation
Indices: 6616395--6616449 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
6616385 AATAATAAAA
6616395 TAAATAAATAATACT-TTAAATT
1 TAAATAAATAA-ACTCTT-AATT
*
6616417 TAAA-AAATTAACTCTTAATT
1 TAAATAAATAAACTCTTAATT
*
6616437 TAAAGAAAATAAA
1 TAAA-TAAATAAA
6616450 TGTAATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 11 0.39
21 7 0.25
22 10 0.36
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAATAAATAAACTCTTAATT
Found at i:6619848 original size:31 final size:31
Alignment explanation
Indices: 6619788--6619853 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6619778 ATTTCAAAAT
* **
6619788 TATATATAAATTATGATTTAATGTGTAATTA
1 TATATATAAATTATAATTTAATGCATAATTA
* * *
6619819 TATATATAAATTTTAATTTTATGCATAATTT
1 TATATATAAATTATAATTTAATGCATAATTA
6619850 TATA
1 TATA
6619854 AGTAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (31 bp):
TATATATAAATTATAATTTAATGCATAATTA
Found at i:6623594 original size:57 final size:58
Alignment explanation
Indices: 6623525--6623633 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 58
6623515 TCATTAGGAA
*
6623525 CTTTCCTAAATAGTTTCACTCCTAACCCATCC-TTTTTGGCTGATTCTAAGGGTGGAG
1 CTTTCCTAAATAGTTTCACTCCTAACCCATCCTTTTTTGGCTAATTCTAAGGGTGGAG
** *
6623582 CTTTCCTAAATAGTTTCACTGGTAACCCATCCTTTTTTTGCTAATTCTAAGG
1 CTTTCCTAAATAGTTTCACTCCTAACCCATCCTTTTTTGGCTAATTCTAAGG
6623634 TTGAGTTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 30 0.64
58 17 0.36
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (58 bp):
CTTTCCTAAATAGTTTCACTCCTAACCCATCCTTTTTTGGCTAATTCTAAGGGTGGAG
Found at i:6635496 original size:8 final size:8
Alignment explanation
Indices: 6635485--6635509 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6635475 TTAATTAATT
6635485 TTTTAAAA
1 TTTTAAAA
6635493 TTTTAAAA
1 TTTTAAAA
6635501 TTTTAAAA
1 TTTTAAAA
6635509 T
1 T
6635510 ATTAGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:6635502 original size:18 final size:18
Alignment explanation
Indices: 6635481--6635530 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
6635471 TCAATTAATT
6635481 AATTTTTTAAAATTTTAA
1 AATTTTTTAAAATTTTAA
* *
6635499 AA--TTTTAAAATATTAG
1 AATTTTTTAAAATTTTAA
6635515 AATTATTTTAATAATT
1 AATT-TTTTAA-AATT
6635531 ATATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 14 0.56
18 2 0.08
19 6 0.24
20 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTTTTTAAAATTTTAA
Found at i:6636659 original size:2 final size:2
Alignment explanation
Indices: 6636652--6636682 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6636642 TGTTCAAATC
*
6636652 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6636683 AAGTGGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6639591 original size:30 final size:31
Alignment explanation
Indices: 6639552--6639611 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
6639542 AGAGGTGGGA
*
6639552 TGGGAAGGGAATAAAAGTTGTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTGTAGGGGAAAAG
* * *
6639583 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTGTAGGGGAAAA
6639612 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.42, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTGTAGGGGAAAAG
Found at i:6639838 original size:9 final size:9
Alignment explanation
Indices: 6639824--6639859 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
6639814 TATAGTTTGA
6639824 TATTCGAAT
1 TATTCGAAT
6639833 TATTCGAAT
1 TATTCGAAT
* *
6639842 GATTCGAGT
1 TATTCGAAT
6639851 TATTCGAAT
1 TATTCGAAT
6639860 CGAAAACTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6639848 original size:18 final size:18
Alignment explanation
Indices: 6639825--6639859 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6639815 ATAGTTTGAT
6639825 ATTCGAATTATTCGAATG
1 ATTCGAATTATTCGAATG
*
6639843 ATTCGAGTTATTCGAAT
1 ATTCGAATTATTCGAAT
6639860 CGAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
ATTCGAATTATTCGAATG
Found at i:6639930 original size:9 final size:9
Alignment explanation
Indices: 6639913--6639943 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6639903 TCGAGTTGAT
6639913 TCGAATAAC
1 TCGAATAAC
*
6639922 TCGATTAAC
1 TCGAATAAC
6639931 TCGAATAAC
1 TCGAATAAC
6639940 TCGA
1 TCGA
6639944 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6649777 original size:26 final size:26
Alignment explanation
Indices: 6649719--6649779 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
6649709 TTGATTAATG
*
6649719 AAATATATTCAAATTATATTATTTTAA
1 AAATA-ATTCAAAGTATATTATTTTAA
6649746 ATAATAATT-AAAGTATATTTATTTTAA
1 A-AATAATTCAAAGTATA-TTATTTTAA
6649773 AAATAAT
1 AAATAAT
6649780 ATAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 13 0.42
27 14 0.45
28 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
AAATAATTCAAAGTATATTATTTTAA
Found at i:6650040 original size:18 final size:18
Alignment explanation
Indices: 6650017--6650056 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6650007 TATAATTTTA
*
6650017 AAAAATA-TATAATACATC
1 AAAAATAGTA-AAAACATC
6650035 AAAAATAGTAAAAACATC
1 AAAAATAGTAAAAACATC
6650053 AAAA
1 AAAA
6650057 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAAATAGTAAAAACATC
Found at i:6650185 original size:31 final size:34
Alignment explanation
Indices: 6650122--6650199 Score: 117
Period size: 32 Copynumber: 2.4 Consensus size: 34
6650112 TAGATGCAAC
*
6650122 TTAACAAGCAAATGTCTCTAAAATAATAACAAAA
1 TTAACAAGAAAATGTCTCTAAAATAATAACAAAA
*
6650156 TTAA-AA-AAAATGTCTTTAAAAT-ATAACAAAA
1 TTAACAAGAAAATGTCTCTAAAATAATAACAAAA
6650187 TTAACAAGAAAAT
1 TTAACAAGAAAAT
6650200 AAGTTTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 13 0.32
32 16 0.40
33 7 0.17
34 4 0.10
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (34 bp):
TTAACAAGAAAATGTCTCTAAAATAATAACAAAA
Found at i:6658027 original size:27 final size:28
Alignment explanation
Indices: 6657997--6658052 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
6657987 GATAAAAGGG
6657997 AAGGGAAAGT-AAAAAAAATTGAAGAGA
1 AAGGGAAAGTAAAAAAAAATTGAAGAGA
6658024 AAGGGAAAGTAAAAAAAAATTGAAGAGA
1 AAGGGAAAGTAAAAAAAAATTGAAGAGA
6658052 A
1 A
6658053 GAATTGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (28 bp):
AAGGGAAAGTAAAAAAAAATTGAAGAGA
Found at i:6661483 original size:15 final size:16
Alignment explanation
Indices: 6661456--6661485 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6661446 CATGTTTGAG
6661456 TTCTAGATTTATATTA
1 TTCTAGATTTATATTA
6661472 TTCTAG-TTTATATT
1 TTCTAGATTTATATT
6661486 CCAACATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
TTCTAGATTTATATTA
Found at i:6666614 original size:20 final size:19
Alignment explanation
Indices: 6666589--6666626 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6666579 TGCCATTGCA
*
6666589 CTGTACATTTATGATCATTT
1 CTGTACATTGATGA-CATTT
6666609 CTGTACATTGATGACATT
1 CTGTACATTGATGACATT
6666627 GTTTCCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (19 bp):
CTGTACATTGATGACATTT
Found at i:6669335 original size:22 final size:21
Alignment explanation
Indices: 6669299--6669353 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
6669289 ACATGACATA
* *
6669299 AAAATAATATGAAAAATAA-TT
1 AAAATAACAT-AAAAAAAATTT
6669320 AAAAT-ACATAAAAAAAATTT
1 AAAATAACATAAAAAAAATTT
6669340 AAAATCAACATAAA
1 AAAAT-AACATAAA
6669354 TGCTTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
20 10 0.34
21 5 0.17
22 7 0.24
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAACATAAAAAAAATTT
Done.